Molecular programs of fibrotic change in aging human lung

Aging is associated with both overt and subclinical lung fibrosis, which increases risk for mortality from viruses and other respiratory pathogens. The molecular programs that induce fibrosis in the aging lung are not well understood. To overcome this knowledge gap, we undertook multimodal profiling of distal lung samples from healthy human donors across the lifespan. Telomere shortening, a cause of cell senescence and fibrosis, was progressive with age in a sample of 86 lungs and was associated with foci of DNA damage. Bulk RNA sequencing confirmed activation of cellular senescence and pro-fibrotic pathways as well as genes necessary for collagen processing with increasing age. These findings were validated in independent datasets for lung and sun-exposed skin, but not other organs including heart, liver and kidney. Cell type deconvolution analysis revealed a progressive loss of lung epithelial cells and an increasing proportion of fibroblasts. Consistent with the observed pro-fibrotic transcriptional profile, second harmonic imaging demonstrated increased density of interstitial collagen in aged human lungs. Furthermore, regions of parenchymal fibrosis were associated with decreased alveolar expansion and surfactant secretion. These findings reveal the transcriptional and structural features of fibrosis and associated physiologic impairments in normal lung aging.

[1]  M. Selman,et al.  Transcriptomic profile of the mice aging lung is associated with inflammation and apoptosis as important pathways , 2021, Aging.

[2]  I. Noth,et al.  Antibody-mediated depletion of CCR10+EphA3+ cells ameliorates fibrosis in IPF , 2021, JCI insight.

[3]  G. Teng,et al.  Molecular mapping of interstitial lung disease reveals a phenotypically distinct senescent basal epithelial cell population , 2021, JCI insight.

[4]  Nicolas Borisov,et al.  Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways , 2021, Frontiers in Genetics.

[5]  Anushya Muruganujan,et al.  The Gene Ontology resource: enriching a GOld mine , 2020, Nucleic Acids Res..

[6]  Y. Oh,et al.  Aging-related changes in the gene expression profile of human lungs , 2020, Aging.

[7]  M. Matthay,et al.  The endogenous capacity to produce proinflammatory mediators by the ex vivo human perfused lung , 2020, Intensive Care Medicine Experimental.

[8]  Irving L. Weissman,et al.  A single-cell transcriptomic atlas characterizes ageing tissues in the mouse , 2020, Nature.

[9]  D. Lynch,et al.  Interstitial lung abnormalities detected incidentally on CT: a Position Paper from the Fleischner Society. , 2020, The Lancet. Respiratory medicine.

[10]  Michael J. Podolsky,et al.  Age-dependent regulation of cell-mediated collagen turnover. , 2020, JCI insight.

[11]  Hyun Je Kim,et al.  Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis. , 2020, The Journal of allergy and clinical immunology.

[12]  P. Wolters,et al.  Peripheral blood leukocyte telomere length is associated with survival of sepsis patients , 2019, European Respiratory Journal.

[13]  G. A. Fleming,et al.  To help aging populations, classify organismal senescence , 2019, Science.

[14]  Hyun J. Kim,et al.  Peripheral blood proteomic profiling of idiopathic pulmonary fibrosis biomarkers in the multicentre IPF-PRO Registry , 2019, Respiratory Research.

[15]  Irving L. Weissman,et al.  A molecular cell atlas of the human lung from single cell RNA sequencing , 2019, Nature.

[16]  P. Kapahi,et al.  From discoveries in ageing research to therapeutics for healthy ageing , 2019, Nature.

[17]  A. Shilatifard,et al.  Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis , 2019, American journal of respiratory and critical care medicine.

[18]  S. Straus,et al.  Rate of normal lung function decline in ageing adults: a systematic review of prospective cohort studies , 2019, BMJ Open.

[19]  M. Zeng,et al.  The Role of S1P and the Related Signaling Pathway in the Development of Tissue Fibrosis , 2019, Front. Pharmacol..

[20]  Atul J. Butte,et al.  Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage , 2018, Nature Immunology.

[21]  Anushya Muruganujan,et al.  PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools , 2018, Nucleic Acids Res..

[22]  Melissa J. Davis,et al.  Single sample scoring of molecular phenotypes , 2018, BMC Bioinformatics.

[23]  M. Serrano,et al.  Targeting senescence , 2018, Nature Medicine.

[24]  Nancy R. Zhang,et al.  Bulk tissue cell type deconvolution with multi-subject single-cell expression reference , 2018, Nature Communications.

[25]  Fabian J Theis,et al.  An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics , 2018, Nature Communications.

[26]  D. Allison,et al.  Senolytics Improve Physical Function and Increase Lifespan in Old Age , 2018, Nature Medicine.

[27]  Yossi Ovadya,et al.  Strategies targeting cellular senescence. , 2018, The Journal of clinical investigation.

[28]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[29]  G. Raghu,et al.  Time for a change: is idiopathic pulmonary fibrosis still idiopathic and only fibrotic? , 2018, The Lancet. Respiratory medicine.

[30]  A. Friedman,et al.  Human immunology studies using organ donors: Impact of clinical variations on immune parameters in tissues and circulation , 2018, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[31]  G. Washko,et al.  Histopathology of Interstitial Lung Abnormalities in the Context of Lung Nodule Resections , 2017, American journal of respiratory and critical care medicine.

[32]  R. Goldschmeding,et al.  Short telomere length in IPF lung associates with fibrotic lesions and predicts survival , 2017, PloS one.

[33]  J. Sznajder,et al.  The Intersection of Aging Biology and the Pathobiology of Lung Diseases: A Joint NHLBI/NIA Workshop. , 2017, The journals of gerontology. Series A, Biological sciences and medical sciences.

[34]  Yufeng Shen,et al.  Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. , 2017, Cell reports.

[35]  Wiggert A. van Cappellen,et al.  Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging , 2017, Cell.

[36]  A. Oberg,et al.  Cellular senescence mediates fibrotic pulmonary disease , 2017, Nature Communications.

[37]  H. Hatabu,et al.  Interstitial Lung Abnormalities Are Associated with Acute Respiratory Distress Syndrome , 2017, American journal of respiratory and critical care medicine.

[38]  Raúl San José Estépar,et al.  Development and Progression of Interstitial Lung Abnormalities in the Framingham Heart Study. , 2016, American journal of respiratory and critical care medicine.

[39]  J. Austin,et al.  Rheumatoid arthritis-associated autoantibodies and subclinical interstitial lung disease: the Multi-Ethnic Study of Atherosclerosis , 2016, Thorax.

[40]  P. Wolters,et al.  Telomere dysfunction in alveolar epithelial cells causes lung remodeling and fibrosis. , 2016, JCI insight.

[41]  Andrew H. Beck,et al.  PharmacoGx: an R package for analysis of large pharmacogenomic datasets , 2015, Bioinform..

[42]  M. Belvisi,et al.  DNA damage response at telomeres contributes to lung aging and chronic obstructive pulmonary disease , 2015, American journal of physiology. Lung cellular and molecular physiology.

[43]  Qing-Yu He,et al.  DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis , 2015, Bioinform..

[44]  O. Eickelberg,et al.  Hallmarks of the ageing lung , 2015, European Respiratory Journal.

[45]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[46]  Yufeng Shen,et al.  Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life , 2014, Cell.

[47]  V. Thannickal,et al.  Reversal of Persistent Fibrosis in Aging by Targeting Nox4-Nrf2 Redox Imbalance , 2014, Science Translational Medicine.

[48]  Michael J. Cronce,et al.  Type 2 alveolar cells are stem cells in adult lung. , 2013, The Journal of clinical investigation.

[49]  K. Atabai,et al.  Always cleave up your mess: targeting collagen degradation to treat tissue fibrosis. , 2013, American Journal of Physiology - Lung cellular and Molecular Physiology.

[50]  E. Blackburn,et al.  Molecular and Cellular Pathobiology The Major Reverse Transcriptase – Incompetent Splice Variant of the Human Telomerase Protein Inhibits Telomerase Activity but Protects from Apoptosis , 2013 .

[51]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[52]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[53]  N. LeBrasseur,et al.  Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders , 2011, Nature.

[54]  K. Kuwano,et al.  Accelerated epithelial cell senescence in IPF and the inhibitory role of SIRT6 in TGF-β-induced senescence of human bronchial epithelial cells. , 2011, American journal of physiology. Lung cellular and molecular physiology.

[55]  P. Lansdorp,et al.  Short telomeres are a risk factor for idiopathic pulmonary fibrosis , 2008, Proceedings of the National Academy of Sciences.

[56]  J. Wain,et al.  The lysophosphatidic acid receptor LPA1 links pulmonary fibrosis to lung injury by mediating fibroblast recruitment and vascular leak , 2008, Nature Medicine.

[57]  C. E. Perlman,et al.  Alveolar expansion imaged by optical sectioning microscopy. , 2007, Journal of applied physiology.

[58]  G. Rubenfeld,et al.  Prediction of death and prolonged mechanical ventilation in acute lung injury , 2007, Critical care.

[59]  G J Roth,et al.  Inhibition of PDGF, VEGF and FGF signalling attenuates fibrosis , 2007, European Respiratory Journal.

[60]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[61]  N. Reichek The Multi-Ethnic Study of Atherosclerosis (MESA) and myocardial function: where is the boundary between risk factor and disease? , 2006, Journal of the American College of Cardiology.

[62]  N. Carter,et al.  A DNA damage checkpoint response in telomere-initiated senescence , 2003, Nature.

[63]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[64]  Brian Seed,et al.  Dynamic imaging of collagen and its modulation in tumors in vivo using second-harmonic generation , 2003, Nature Medicine.

[65]  M. Matthay,et al.  Assessment of lungs rejected for transplantation and implications for donor selection , 2002, The Lancet.

[66]  R. Cawthon Telomere measurement by quantitative PCR. , 2002, Nucleic acids research.

[67]  J. Bhattacharya,et al.  [Ca(2+)](i) oscillations regulate type II cell exocytosis in the pulmonary alveolus. , 2000, American journal of physiology. Lung cellular and molecular physiology.